Most current models of sequence evolution assume that all sites a protein evolve under the same substitution process, characterized by 20 × matrix. Here, we propose to relax this assumption developing Bayesian mixture model allows amino-acid replacement pattern at different alignment be described distinct processes. Our model, named CAT, assumes existence processes (or classes) differing their equilibrium frequencies over residues. Through use Dirichlet process prior, total number classes...

Abstract Motivation: A variety of probabilistic models describing the evolution DNA or protein sequences have been proposed for phylogenetic reconstruction molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as test their ability jointly improve and dating accuracy. Results: We propose software package, PhyloBayes 3, which can be used conducting Bayesian analyses, using large amino acid replacement nucleotide...

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite models. Consequently, users these software packages are simultaneously forced to use number programs given study, while also lacking the freedom explore models that have not been implemented by developers those programs. We developed new open-source package, RevBayes, address problems. RevBayes is entirely based on probabilistic graphical models, powerful generic framework specifying analyzing...

In the Bayesian paradigm, a common method for comparing two models is to compute Bayes factor, defined as ratio of their respective marginal likelihoods. recent phylogenetic works, numerical evaluation likelihoods has often been performed using harmonic mean estimation procedure. present article, we propose employ another method, based on an analogy with statistical physics, called thermodynamic integration. We describe implementation, and show analytical examples that this yields reliable...

Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that tree is accurate. Systematic errors, such as Long Branch Attraction (LBA) artefact, can be misleading, particular when taxon sampling poor, or outgroup distant. In an otherwise consistent probabilistic framework, systematic errors traced back model mis-specification problems, which...

Almost a decade ago, new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly two major groups protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) Lophotrochozoa annelids, molluscs, platyhelminths, brachiopods, rotifers). However, it received little additional support. In fact, several multigene analyses strongly argued against this phylogeny. These latter studies were based on large amount...

Several models have been proposed to relax the molecular clock in order estimate divergence times. However, it is unclear which model has best fit real data and should therefore be used perform dating. In particular, we do not know whether rate autocorrelation considered or prior on times used. this work, propose a general bench mark of alternative relaxed models. We reimplemented most already existing models, including popular lognormal model, as well various choices for (birth–death,...

Abstract Motivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach improving the robustness phylogenetic reconstructions in presence saturation. However, such profile mixture models were introduced only Bayesian context, and are not yet available maximum likelihood (ML) framework. In addition, these perform well on large alignments, from which they can reliably learn...

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted sister group to remaining animals, consistent with conventional view that last common ancestor was relatively simple and more body plans arose later in evolution. However, this premise has recently challenged by analyses of genomes comb...

Genome-scale data sets result in an enhanced resolution of the phylogenetic inference by reducing stochastic errors. However, there is also increase systematic errors due to model violations, which can lead erroneous phylogenies. Here, we explore impact on eukaryotic phylogeny using a set 143 nuclear-encoded proteins from 37 species. The initial observation was that, despite impressive amount data, some branches had no significant statistical support. To demonstrate that this lack mutual...

The relationships at the root of animal tree have proven difficult to resolve, with current debate focusing on whether sponges (phylum Porifera) or comb jellies Ctenophora) are sister group all other animals [1-5]. choice evolutionary models seems be core problem because Porifera tends emerge as ("Porifera-sister") when site-specific amino acid differences modeled (e.g., [6, 7]), whereas Ctenophora emerges ("Ctenophora-sister") they ignored [8-11]). We show that two key phylogenomic datasets...

▪ Abstract The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction molecular phylogenies. Access to whole-genome means that phylogenetic analysis can now be performed at different levels, such as primary sequences and gene order, allowing reciprocal corroboration results. We critically review kinds phylogenomic methods currently available, paying particular attention method reliability. Our emphasis on because these are most advanced. discuss...

Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of acids. However, site evolution is highly heterogeneous depends on many factors: genetic code; solvent exposure; secondary tertiary structure; function; etc. These impact pattern and, in most cases, not enough to represent all complexity evolutionary processes. This paper explores maximum-likelihood framework phylogenetic mixture combine...

The comparative approach is routinely used to test for possible correlations between phenotypic or life-history traits. To correct phylogenetic inertia, the method of independent contrasts assumes that continuous characters evolve along phylogeny according a multivariate Brownian process. diffusion processes have also been describe time variations parameters substitution process, such as rate ratio synonymous nonsynonymous substitutions. Here, we develop probabilistic framework testing...

Abstract Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives vertebrates. In direct contradiction with long accepted view Euchordates, this new phylogenetic hypothesis for chordate evolution has been object some skepticism. We assembled an expanded dataset focused on deuterostomes. Maximum‐likelihood using standard models and Bayesian CAT site‐heterogeneous mixture model amino‐acid replacement both provided unequivocal support...

We combined the category (CAT) mixture model (Lartillot N, Philippe H. 2004) and nonstationary break point (BP) (Blanquart S, Lartillot N. 2006) into a new model, CAT–BP, accounting for variations of evolutionary process both along sequence across lineages. As in CAT, implements distinct Markovian processes substitution distributed among sites, thus accommodating site-specific selective constraints induced by protein structure function. Furthermore, as BP, these are nonstationary, their...

Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number phylogenetically reliable characters was main limitation traditional phylogenies based on morphology. With advent molecular data, this problem replaced by another one, statistical inconsistency, which stems from erroneous interpretation convergences induced multiple changes. analysis alignments rich in both genes species, combined with probabilistic...

Modeling the interplay between mutation and selection at molecular level is key to evolutionary studies. To this end, codon-based models have been proposed as pertinent means of studying long-range patterns are widely used. However, these approaches not yet consolidated results from amino acid phylogenetic studies showing that acting on proteins displays strong site-specific effects, which translate into heterogeneous propensities across columns alignments; related codon-level instead...

Phylogenomic analyses of ancient relationships are usually performed using amino acid data, but it is unclear whether acids or nucleotides should be preferred. With the 2-fold aim addressing this problem and clarifying pancrustacean relationships, we explored signals in 62 protein-coding genes carefully assembled by Regier et al. 2010. reference to pancrustaceans, data set infers a highly supported nucleotide tree that substantially different corresponding, poorly supported, one. We show...

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along phylogeny traced by ancestors extant species. presence lateral gene transfer, however, this may not be case, because species lineage from which a was transferred gone extinct or been sampled. Because it feasible specify reconstruct complete all species, we must describe genes outside represented modeling speciation dynamics that gave rise phylogeny. We demonstrate if number sampled small...

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of information into unified statistical analysis. One might expect this improve the agreement between rocks and clocks but is not necessarily case. We explore reasons for such discordance using mammalian dataset with rich molecular, morphological fossil information. There strong conflict in morphology molecules under standard stochastic models. This causes TED push divergence events back time when...

Violation of the molecular clock has been amply documented, and is now routinely taken into account by dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to evolution life-history traits, such as body size or generation time. Life-history can be reconstructed using Brownian models. However, resulting estimates are typically uncertain, potentially sensitive underlying assumptions. As way obtaining more accurate ancestral trait divergence...